BiopsyTrees

Same as ExampleClones but with biopsies predicted at internal nodes

datasets

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

BiopsyTrees function

A tibble of airrClone and phylo objects output by getTrees.<ul>
<li><code>clone_id</code>: Clonal cluster</li>
<li><code>data</code>: List of airrClone objects</li>
<li><code>seqs</code>: Number of sequences</li>
<li><code>trees</code>: List of phylo objects</li>
</ul>

Format

Example Ig lineage trees with biopsy reconstructions. — BiopsyTrees

Example Ig lineage trees with biopsy reconstructions.

BiopsyTrees: Example Ig lineage trees with biopsy reconstructions.

Description

Usage

Arguments

Format

See Also